short note on prokaryotic gene structure

2.  Gene is the unit of heredity
 Portion of chromosome encoding a functional RNA or protein
 Simple in prokaryotes
 Minimal amount of regulatory sequences to control gene
expression

3.  Simple structure
 Small genome(0.5-10 million base pairs)
 No introns
 Genes are called as open reading frames(ORFs)
 High coding density
 Sometimes Nested
 Some are too short ~60bp

5. 1) recognition region ( 50 bp)
2) transcription initiation site
3) untranslated region
4) translation initiation
5) coding region
6) translation stop site
7) untranslated region
8) translation stop site

6.  The upstream elements from the start of the coding
region include promoter elements.
 Nearly 50 to 100 ntds upstream of the start codon, is
the first nucleotide at which transcription initiates, it
means, it is at this site the first nucleotide is
incorporated into the transcribed RNA.
 The site is called transcriptional initiation site or START.

7.  Nearly 10 nucleotides upstream of the start, there is a
sequence called TATAAT or Pribnow box.
 Any nucleotide present on the left of the start is denoted by
(-) symbol and the region is called upstream element. The
numbers are written as -10, -20, -35 etc.
 The start site is the first ntds and symbolized by +1, any
sequence to the right of the start is called down stream
elements and numbered as +10, +35 and so on.

8.  At –35 there is another consensus sequence TTGACA.
 These two sequences are the most important promoter
elements, for if there is any change in their sequence and
position, transcriptional initiation suffers.
 The meaning of a promoter essentially is a distinct sequence
module recognized by RNA polymerase (as a holozyme), bind
to the sequence tightly and initiate transcription by unwinding
the helically coiled DNA into transcriptional bubble.

9.  The said sequences not only facilitate the binding
of the enzyme and also provide sequence
information for the site at which the enzyme to
initiate transcription.
 If any one of the consensus sequences is
deleted or changed drastically, the enzyme won’t
bind, even if it binds, it initiates transcription at
different positions.

10. PROMOTER
-200 -65 -60 -35 -10 +1
I----------I----//---I---------------I--------I------I--I----A >
Enhancers Activator TTGACA TATAT
TGTGA--CTCACA
Consensus promoter sequence in E.coli:
-35 TCTTGACAT—11-15—TATAAT-5-8 InR +1A(G/T/C)
RNA polymerase binding region-
-35 --10 +1----->
TTGACA-------TATAAT----C A T-----

11.  Ribosome binding site
 A shot sequence upstream to the start site
 5’-CCUCCU-3’